A cost-effective and field-ready potentiostat that poises subsurface electrodes to monitor bacterial respiration

Here, we present the proof-of-concept for a subsurface bioelectrochemical system (BES)-based biosensor capable of monitoring microbial respiration that occurs through exocellular electron transfer. This system includes our open-source design of a three-channel microcontroller-unit (MCU)-based potentiostat that is capable of chronoamperometry, which laboratory tests showed to be accurate within 0.95 ± 0.58% (95% Confidence Limit) of a commercial potentiostat. The potentiostat design is freely available online: http://angenent.bee.cornell.edu/potentiostat.html. This robust and field-ready potentiostat, which can withstand temperatures of -30°C, can be manufactured at relatively low cost ($600), thus, allowing for en-masse deployment at field sites. The MCU-based potentiostat was integrated with electrodes and a solar panel-based power system, and deployed as a biosensor to monitor microbial respiration in drained thaw lake basins outside Barrow, AK. At three different depths, the working electrode of a microbial three-electrode system (M3C) was maintained at potentials corresponding to the microbial reduction of iron(III) compounds and humic acids. Thereby, the working electrode mimics these compounds and is used by certain microbes as an electron acceptor. The sensors revealed daily cycles in microbial respiration. In the medium- and deep-depth electrodes the onset of these cycles followed a considerable increase in overall activity that corresponded to those soils reaching temperatures conducive to microbial activity as the summer thaw progressed. The BES biosensor is a valuable tool for studying microbial activity in situ in remote environments, and the cost-efficient design of the potentiostat allows for wide-scale use in remote areas.     

ORBIT: an integrated environment for user-customized bioinformatics tools

MOTIVATION: There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. RESULTS: We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.     

Computer graphics with computerized tomography for functional neurosurgery

A computer graphics technique for computer-assisted stereotactic surgery is presented. The program is designed to aid the surgeon by presenting an on-line graphics display of stereotactic probes and electrodes superimposed on cross sections of the human brain stem. This technique simulates an otherwise blind surgical procedure on a graphics screen for use during surgery. An earlier system based around the DEC MINC-11 BA computer system has been used by the authors for the performance of stereotactic surgery with conventional ventriculography. This system has been upgraded and is now configured about an even more compact microprocessor-based hardware system with expanded graphics capabilities, which also allows its use with computerized tomography.     

Microelectrode arrays and application to biosensing devices

An electrochemical microanalytical system consisting of a microelectrode array, a micromachined flow-through assembly, and a multichannel potentiostat were constructed for highly sensitive biosensing. Thin-film platinum microelectrode arrays consisting of four interdigitated microelectrodes (IDAs), which are spaced in the sub-micrometer range, were fabricated using silicon technology. On top of this chip, a micromachined flow-through cell was mounted. Using a home made miniaturized multipotentiostat, amperometric measurements of the individual electrodes at different and changing potentials, respective to a single reference electrode, were performed simultaneously. The signal generation, signal processing and the analytical system were controlled by a computer (PC type) and special software. An improved sensor sensitivity was achieved by multielectrode detection and averaging of the IDA responses.

By applying both the oxidation and reduction potentials of reversible redox molecules to pairs of the interdigitated electrodes, an increased current generation can be observed. Thus the steady state current of mediators such as benzoquinone can be amplified by a factor of 30 compared with conventional electrodes. This measuring principle was applied to determine of the activity of hydrolases by detecting the enzyme generated p-aminophenol in the nanomolar range. By combining both, the averaging and the recycling procedures, the detection limit of amperometric biosensing devices may be lowered by about one and a half orders of magnitude.     

An improved technique for dental alloy etching with a potentiostatic device

Since a good retention of direct bonded retainers onto abutment teeth is the primary requirement for the fabrication of etched fixed partial dentures, successful formation of a micromechanical retentive architecture on the bonding surface is one of the most important procedures. For creating such a retentive dendritic pattern on nonprecious metal, a 2-electrode electrolytic method has been used. This equipment consists of a low-voltage DC power supply and two electrodes, namely, a working and a counter one. However, the current and voltage should be monitored during the entire processing time and the etching area must be pre-estimated. A potentiostat has been used to automatically stabilize the voltage across the working electrode and reference electrode by adjusting the current, as commonly employed in electro-chemical technology. A 3-electrode corrosion device originally developed for laboratory research was adapted for dental retainer etching in this study. The results revealed that the etching of dental nonprecious metal (Ni-Cr-Be alloy) could successfully be performed by using the system with a potentiostat. Moreover, the working potential was found to be approximately 1.3 volts by taking the midpoint between the breakdown and the critical potentials for passivation on the potentiostatic anode polarization curves. The optimal exposure time has been found to be in a range of 3 to 5 minutes and 4 minutes to be ideal as determined by SEM microphotographic observation which showed a uniform dendritic pattern with regular lattice form of alternating ridges and valleys.(ABSTRACT TRUNCATED AT 250 WORDS)     

A tool for the morphological analysis of mixtures of lipids and water in computer simulations

When analyzing computer simulations of mixtures of lipids and water, the questions to be answered are often of a morphological nature. They can deal with global properties, like the kind of phase that is adopted or the presence or absence of certain key features like a pore or stalk, or with local properties, like the local curvature present at a particular part of the lipid/water interface. While in principle all of the information relating to the global and local morphological properties of a system can be obtained from the set of atomic coordinates generated by a computer simulation, the extraction of this information is a tedious task that usually involves using a visualization program and performing the analysis by eye. Here we present a tool that employs the technique of morphological image analysis (MIA) to automatically extract the global morphology—as given by Minkowski functionals—from a set of atomic coordinates, and creates an image of the system onto which the local curvatures are mapped as a color code.     

Gifa V. 4: A complete package for NMR data set processing

Summary The Gifa program is designed for processing, displaying and analysing 1D, 2D and 3D NMR data sets. It has been constructed in a modular fashion, based on three independent modules: a set of commands that perform all the basic processing operations such as apodisation functions, a complete set of Fourier Transforms, phasing and baseline correction, peak-picking and line fitting, linear prediction and maximum entropy processing; a set of command language primitives that permit the execution of complex macro commands; and a set of graphic commands that permit to build a complete graphic user interface, allowing the user to interact easily with the program. We have tried to create a versatile program that can be easily extended according to the user's requirements and that is adapted to a novice as well as an experienced user. The program runs on any UNIX computer, with or without graphic display, in interactive or batch mode.     

The role of computed tomographic and digital radiographic techniques in stereotactic procedures for electrode implantation and mapping, and lesion localization

This paper describes a computer-based system for analyzing stereotactic CT scans and angiograms. Simple Plexiglas frames containing metallic marker pellets and rods are affixed to the sides of the frame during CT scanning and angiography. The images of these markers are recognized by the computer program and used to compute the frame coordinate system. Coordinates of a lesion on CT and angiogram images may be readily computed and coordinate sets specified by the operator may be displayed on the imager, along with positions of implanted electrodes and a numerical indication of recorded activity for each site.     

A flexible new computer program for handling DNA sequence data.

A compact new computer program for handling nucleic acid sequence data is presented. It consists of a number of different subsets, which may be used according to a given code system. The program is designed for the determination of restriction enzyme and other recognition sites in correlation with translation patterns, and allows tabulation of codon frequencies and protein molecular weights within specified gene boundaries. The program is especially designed for detection of overlapping genes. The language, is FORTRAN and thus the program may be used on small computers; it may also be used without any prior computer experience. Copies are available on request.     

Insect electroantennogram responses to semiochemicals recorded with an inexpensive personal computer

ABSTRACT. . A circuit and accompanying program that allow an inexpensive personal computer to replace an expensive storage oscilloscope in displaying electroantennogram (EAG) recording is described. The maximum amplitude of the EAG is calculated automatically by the computer and appears as an alphanumeric display on the monitor screen. Because the entire EAG trace is stored by the computer, parameters of the EAG trace other than the maximum amplitude are also available for analysis, such as voltages at specified times after antennal stimulation.     

Automation of conformational analysis and other molecular modeling calculations

A software system has been developed for facilitating modeling calculations on large numbers of molecules. Using the system, it is possible to subject one or more molecules to a series of calculations, each requiring use of a different computer program. No user intervention is required: where necessary, output from one program is used automatically as input to the next. Names are assigned to output files automatically and in a systematic manner. As an example, the system can be used to perform a succession of calculations aimed at identifying the major low-energy conformers of each of a set of molecules, starting only from their chemical connectivities. The reliability of the results has been tested by calculations on 40 molecules taken from the Cambridge Structural Database. The observed crystal structure geometry could be found for the majority of these molecules.     

The use of differential measurements with a glucose biosensor for interference compensation during glucose determinations by flow injection analysis

A novel detection system for the determination of glucose in the presence of clinically important interferents, based on the use of dual sensors and flow-injection analysis (FIA), is described. The normalisation methodology involves measurement of the interference signal at a reference sensor; this signal can then be subtracted from the glucose sensor signal (post-run) to give a corrected measurement of the glucose concentration. The detection system consists of a thin layer cell with dual glassy carbon working electrodes. One electrode was surface modified to act asglucose biosensor by immobilisation of glucose oxidase (GOx) (from Aspergillus niger) with 1% glutaraldehyde and bovine serum albumin. The second electrode (glucose oxidase omitted) was utilised to measure the interference signal responding only to electroactive species present in the injected sample. A computer controlled multichannel potentiostat was used for potential application and current monitoring duties. The sensor responses were saved in ASCII format to facilitate post-run analysis in Microsoft Excel. Cyclic voltammetry (CV) was utilised to investigate the manner in which the interference signal contributed to the total signal obtained at the biosensor in the presence of glucose. The kinetic parameters I_max and the apparent Michaelis-Menten constant, K′_m, were calculated for the sensor operating under flow-injection conditions.     

Protein Structure Discovery: software package to perform computational proteomics tasks

Software-information system Protein Structure Discovery was developed. The system can be used for the wide range of tasks in the field of computer proteomics including prediction of function, structure and immunological properties of proteins. A specially created section of the system allows evaluating the quantitative and qualitative effects of mutations on the structural and functional properties of proteins. There are 19 of different programs integrated into the system, including the database of protein functional sites PDBSite, a PDBSiteScan program for the prediction of functional sites in three-dimensional structures of proteins, and WebProAnalyst program for the quantitative analysis of the structure-activity relationship of proteins. Protein Structure Discovery program has a Web interface and is available for users through the Internet (http://www-bionet.sscc.ru/psd/). For example, binding sites of zinc ion and ADP showed high stability of the method to errors PDBSiteScan reconstruction of spatial structures of proteins in the recognition of functional sites in model structures.     

Quantitative evaluation of the performance of different electrical tomography devices.

Two widely used electrical tomography systems, the Sheffield Mark I and the DAS-01P, were quantitatively evaluated and compared to the newly developed Goe-MF system. The performance was quantified using a hardware phantom which closely matches the real input and transfer impedances of the human thorax and allows measurements equivalent to different states of lung inflation. Our results demonstrate that adequate averaging is necessary for noise reduction for the Mark I and especially for the DAS-01P system to get meaningful results even in visualizing maximal respiratory manoeuvres. The Goe-MF system showed a notably improved signal-to-noise ratio which allows also dynamic measurements at low levels of lung volume changes, e.g., in intensive care lung injury patients.     

Telemetric recording of neuronal activity

A telemetric system is described which allows the wireless registration of extracellular neuronal activity and vocalization-associated skull vibrations in freely moving, socially living squirrel monkeys (Saimiri sciureus). The system consists of a carrier platform with numerous guiding tubes implanted on the skull. Custom-made microdrives are mounted on the platform, allowing the exploration of two electrode tracks at the same time. Commercially available quartz-insulated platinum-tungsten microelectrodes are used. The electrodes can be moved over a distance of 8-10 mm by turning a screw on the microdrive. Vocalization-associated skull vibrations are recorded with a piezo-ceramic element. Skull vibration signal and the signals from the two microelectrodes are fed into separate transmitters having different carrier frequencies. The signals are picked up by an antenna in the animal cage and are sent to three receivers in the central laboratory. Here, the signals are transferred via an analog/digital interface to a personal computer for data analysis and to a video recorder for long-term storage. The total weight of the head mount including carrier platform, microdrive, electrodes, skull vibration sensor, three transmitters, and protection cap is 32 g. The transmitters are powered with two rechargeable lithium batteries, allowing about 8 h of continuous recording. Reliable signal transmission is obtained over a distance of about 2 m. Recording stability allows to follow the activity of specific neurons up to several hours, with no movement artefacts during locomotion.     

Boundary conditions at the cartilage-synovial fluid interface for joint lubrication and theoretical verifications

The objective of this study is to establish and verify the set of boundary conditions at the interface between a biphasic mixture (articular cartilage) and a Newtonian or non-Newtonian fluid (synovial fluid) such that a set of well-posed mathematical problems may be formulated to investigate joint lubrication problems. A "pseudo-no-slip" kinematic boundary condition is proposed based upon the principle that the conditions at the interface between mixtures or mixtures and fluids must reduce to those boundary conditions in single phase continuum mechanics. From this proposed kinematic boundary condition, and balances of mass, momentum and energy, the boundary conditions at the interface between a biphasic mixture and a Newtonian or non-Newtonian fluid are mathematically derived. Based upon these general results, the appropriate boundary conditions needed in modeling the cartilage-synovial fluid-cartilage lubrication problem are deduced. For two simple cases where a Newtonian viscous fluid is forced to flow (with imposed Couette or Poiseuille flow conditions) over a porous-permeable biphasic material of relatively low permeability, the well known empirical Taylor slip condition may be derived using matched asymptotic analysis of the boundary layer at the interface.     

COLONY: a program for parentage and sibship inference from multilocus genotype data

Pedigrees, depicting genealogical relationships between individuals, are important in several research areas. Molecular markers allow inference of pedigrees in wild species where relationship information is impossible to collect by observation. Marker data are analysed statistically using methods based on Mendelian inheritance rules. There are numerous computer programs available to conduct pedigree analysis, but most software is inflexible, both in terms of assumptions and data requirements. Most methods only accommodate monogamous diploid species using codominant markers without genotyping error. In addition, most commonly used methods use pairwise comparisons rather than a full-pedigree likelihood approach, which considers the likelihood of the entire pedigree structure and allows the simultaneous inference of parentage and sibship. Here, we describe colony, a computer program implementing full-pedigree likelihood methods to simultaneously infer sibship and parentage among individuals using multilocus genotype data. colony can be used for both diploid and haplodiploid species; it can use dominant and codominant markers, and can accommodate, and estimate, genotyping error at each locus. In addition, colony can carry out these inferences for both monoecious and dioecious species. The program is available as a Microsoft Windows version, which includes a graphical user interface, and a Macintosh version, which uses an R-based interface.     

A novel laboratory fermentation equipment allowing to obtain gas exchanges and doubling time for the study of yeast metabolism

This equipment is composed of a commercially available fermenter and a set of home-made devices. Successively are described: 1) a very simple and inexpensive interface in order to use the not galvanically isolated output voltages of the regulation block; 2) an electric modification of a nephelometer in order to obtain a range automatic changeover system; 3) an original method with three turbine flow-rate meters combined with an oxygen trap to obtain gas exchanges; 4) another original method of gas calibration with effervescent tablets. A culture of a wild type strain of Saccharomyces cerevisiae is shown, as an example, with the calculated culture parameters and their standard deviations.     

Using Eye Movement to Control a Computer: A Design for a Lightweight Electro-Oculogram Electrode Array and Computer Interface

This paper describes a human-computer interface based on electro-oculography (EOG) that allows interaction with a computer using eye movement. The EOG registers the movement of the eye by measuring, through electrodes, the difference of potential between the cornea and the retina. A new pair of EOG glasses have been designed to improve the user''s comfort and to remove the manual procedure of placing the EOG electrodes around the user''s eye. The interface, which includes the EOG electrodes, uses a new processing algorithm that is able to detect the gaze direction and the blink of the eyes from the EOG signals. The system reliably enabled subjects to control the movement of a dot on a video screen.